Stargate Atlantis: S7 The Fossil Key Part Three: Mesopredator Release
by the morrighan
Summary: These stories are a continuation from the season 6 stories to be found in the T section. This is the third story of five. A daring rescue leaves Atlantis vulnerable to internal attack. Will John Sheppard return in time to save the city from itself?
1. Chapter 1

Stargate Atlantis: S7 The Fossil Key

Part Three: Mesopredator Release

Moira O'Meara woke.

Consciousness returned slowly, rising from an enforced slumber. She stirred but couldn't move, not really. She opened her eyes. Everything was bleary and too bright. A dull pain was thudding in her head. She moved. She was still strapped to the bed. She recognized the confines of the infirmary. She tried to remember what had happened to her. Her memory was like a cobweb of drugs and emotions, indistinct and broken.

She opened her eyes again, not realizing she had closed them. She turned her head to the side and stared, startled. There was a man sitting nearby. She blinked, trying not to panic as the memory of what had been done to her became sharp and distinct. She began to struggle, but froze. The man was just sitting there, and it wasn't Carson. This man was clad in black BDUs and his handsome face was serious, familiar. The name was just out of her reach until he licked his lips and it came to her.

"John? John…" Her voice was thick, congealed by tears and screams.

She wondered if she had misidentified him, but no, he was John Sheppard. Except that if he was John he would have rushed to aid her, to free her from the restraints. Wouldn't he? Her heart sank as she realized that, however real he appeared he must be a hallucination.

He had to be a hallucination. Didn't he?

"They've all turned against you, Moira," he said in a quiet voice, a familiar voice. "All but me."

Moira stared through a haze of tears, blinking to try to clear her sight. She watched as he stood, took a few steps towards her. He was standing half in shadow, half in light. His beauty was mitigated by the darkness across half of his face, across his dark clothes. "John? I…I know," she said softly, still uncertain if he was real or not.

"And now you doubt me?" he asked, staring down at her.

"I…I can't do this anymore, John. I can't. We, we have to end this now. It's for the best." Her voice wavered with tears and sorrow and conviction.

His green eyes narrowed as he took another step towards her. "Do you doubt me?" he repeated quietly. There was a rough edge to his voice.

"No." She blinked away tears. Her vision was blurring again and she was losing focus, losing her focus on that handsome face and stern regard. "I doubt myself…and now…"

"Now they've turned against you and betrayed you. Every one of them, in some way has betrayed you. Even the ones you would least suspect. Right? Except me, Moy. Except for me." He stepped closer and leaned down to her. "Except for me, Moy. Remember that."

"John? John, please, please…no, no!" Moira stared in horror as John turned and walked away from her. He just walked away from her, to be replaced by Carson Beckett.

The doctor smiled. "Still seeing things, Moira? Don't worry. We can cure that. We will cure that once and for all."

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John Sheppard flew.

Of course it wasn't really flying since he was underwater, but the mechanics were nearly the same as he guided the Puddle Jumper unerringly towards its target. The ship's lights played across the ocean depths, revealing startled schools of brightly-colored fish and jungles of algae and coral. With a glance he checked navigation and saw that he was rapidly approaching his target.

Just as something else was approaching the same target from the other side.

John frowned, seeing the second blip coming from the opposite direction. He wondered if it could be one of Rodney's whales, but realized it was too small for that, nor was it organic. That left only one other option.

The fuglies.

John cursed to himself and picked up speed. He had no idea that the fuglies had underwater vessels, but now he knew. Somehow they were tracking the other Jumper and pursuing it. And if they could find the Jumper they would find Atlantis. John tapped his earpiece. "Reynolds, copy? Reynolds, this is Sheppard. How far away is the bogey from your position?"

"Colonel!" Jason Reynolds sounded relieved and worried all at once. "Before we lost power our last reading had him at a nautical mile but heading for us. Sir?"

"I will reach you first, major. I was gonna tow you home but I've had a better idea. Do you have any power at all?"

"Negative, sir. She's dead in the water."

"Crap. Okay. Change of plans. I'm going to extend the shield and create a tunnel for you two to cross over into my ship on my mark. But be damn quick about it. Understood?"

"Yes, sir. What about the fugly?"

"Let me worry about the fugly. Just get ready to haul ass on my mark."

"What are you going to do?" Ronon Dex asked. He was relieved to hear Sheppard's voice even though they hadn't been rescued quite yet.

John smiled. "We're gonna blow them out of the water."

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Rodney McKay snorted.

He jerked awake, sitting up and blinking rapidly. He had fallen asleep on a console in the control room. He rubbed his eyes, his face. He couldn't remember when he had gotten a good night's sleep. It had been a few days, at least. He eyed the monitors.

"Shit!" He grabbed his earpiece and tapped it. "Sheppard! Sheppard, do you copy?"

"You don't have to shout, McKay." John sounded irritated.

"Sorry! There's a—"

"Fugly in the water heading for the Jumper, yeah, got it. Stand by. Once my guys are clear we're gonna stage an accident and then get back to Dodge. Keep that porch light on."

"You're going to what? Sheppard? Sheppard, repeat!" Rodney tapped the earpiece but only static buzzed like an angry bee. "Damn it!" He swiveled in his chair as Amelia Banks-Dex approached, carrying a tray of sandwiches. "Oh, thank God!"

"Were you in contact with Colonel Sheppard?" she asked, setting the tray near the ravenous physicist.

"Yes! He's almost reached them but there's a fugly ship in the water approaching fast! But John's got a plan to take care of it." He grabbed a sandwich and bit into it. "We need to keep power levels low until they get back," he said round the mouthful of food. "It's going to take careful timing to get them back into the city."

"We can do it," Amelia assured, grabbing a sandwich. "Do you have an ETA?"

"No…but we can track them here." He tapped a screen. Three blips were on it. The picture flickered. Rodney tapped it again, restoring it. "Great, that's just what we don't need, another damn power fluctuation! Hey, where were you earlier?"

"I was helping Carson. The two big ships haven't changed position yet." She sat at a console and tapped on the keyboard, updating the screen. "What is the Colonel's plan?"

"I don't know…but knowing John it probably involves something exploding."

"I just hope it's the fuglies and not us," Amelia murmured.

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Jason sagged with relief, but he moved to his feet. Ronon was already standing and the Satedan headed for the back of the Jumper. Jason checked the controls once more. "Nothing. No power at all! Not even a whimper. Oh shit." He stared out the viewport.

In the distance lights could be seen, scouring the ocean floor. They were odd amber beams and Jason knew they weren't a Jumper's lights, which could only mean one thing: the fuglies were getting closer.

"Come help me with the door. We'll have to use the manual release," Ronon said, gripping the handle in readiness. He wasn't about to die down on the ocean floor, not without a fight. He smiled, feeling a resurgence of his old confidence and stubbornness.

"They're coming. They must have tracked us. That ship over the mainland must have tracked us after they pulled up the landing party. Then they dropped a submersible to find us."

"Doesn't matter. Sheppard's got a plan. Come and help me with this door," Ronon repeated, but the other man seemed glued to the spot watching the spooky amber lights get closer, closer.

"It does matter! If they can find us they will find—"

"No they won't!" Ronon barked, cutting off the other man's panic. "Sheppard will take care of it. Help me get this damn door ready to open once he gets here! Reynolds!"

Jason jumped at the ordering tone. He whirled, about to say something but changed his mind. He nodded and joined Ronon at the door.

All that the two men could do now was to wait.

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Carson slammed his palm on the device, but the power was still weak and the dial would only go halfway. The lights flickered, flickered and then dissolved as the emergency lights took over for them. He cursed, crossed the infirmary and tapped his earpiece. "Rodney! What the bloody hell is going on?"

"Carson?" Rodney asked, startled by the doctor's vehement tone.

"I can't work under these conditions!"

"Oh! I've had to cut power levels in preparation for John's return. We need to be able to access the shield to allow the Jumper to return safely."

"I need full power in here, damn it! I am right in the middle of a delicate procedure." He glanced over at his patient. She was moaning softly, half in and out of consciousness.

"Sorry, Carson, but this takes precedence. Wait, is this about Moira? What are you—"

"Fine! I will just have to wait then, or find an alternate power source!" Carson stumbled and caught himself. He glanced round, feeling a weird disconnection with his body. He stared at Moira who was prone on a bed, strapped to it. "Good lord! What have I done? What have I done? Moira!" He rushed to the biologist and unstrapped one wrist, horrified at her state, at the medical devices on the tray next to her. "I've got to get you out of here now!"

Moira stirred, consciousness fluttering. She weakly moved, trying to see past the haze as Carson was freeing her wrist. His fingers were cold, so cold she felt a shiver. "Carson? Carson, please, please help me…" she whispered, flexing her fingers awkwardly.

"Forgive me, Moira, forgive me!" Carson paused. Moira was staring behind him. Her brown eyes widened with focus and dread.

A chill breath snaked up the back of his neck.

Moira tried to warn him but no words came.

Coldness began to creep along Carson's limbs and he struggled, struggled with some unseen force that was wrapping itself around him. It was hard to move. His fingers felt numb, unable to bend and his hold slipped off the strap. He glanced at the tray. The silver surface reflected a shadow behind him, a shadow of light and translucence. He caught a glimpse of a beautiful, cold woman until she melted into him.

The coldness encompassed him, devoured him. He was encased in ice, a prisoner in his own body. He was helpless to act. He could only watch through a chilling filter.

Carson restored the restraint onto Moira's wrist.


	2. Chapter 2

Stargate Atlantis: S7 The Fossil Key

Part Three: Mesopredator Release2

Moira woke.

Memory was a gauzy mess of emotion and pain and she couldn't tell what was real or what wasn't real. She fought to clear her mind as she struggled weakly on the bed. She was still restrained and the straps were biting into her flesh although they were padded. She opened her eyes. Lights swam in a blur above her, but they were dimmer now, darker.

"You don't love me. Is that it?"

Moira gasped. She looked over at the sound of the male voice. There was a man seated in a chair near the bed. His legs were crossed at the ankles. His hands were folded in his lap as if he was conducting an interview. He was handsome, impossibly handsome in his black BDUs and his scruffy jaw, dark brown hair, keen green eyes and perfect, perfect lips that were forming a scowl that was both sexy and dangerous.

She stared, unable to remember his name for a moment. "You…John. John Sheppard. John? No." She couldn't tell if he was real or not.

"No?" he questioned, one brow rising in derision or suspicion. "What does that mean?"

Moira tried to pull free but the restraints were tight. She knew that if John was really here he would help her. Wouldn't he? "It means…it means I love you, but that's not the point and never has been. I can, I can deal with that."

"What can't you deal with? Ah, let me guess. Them? Or me?"

Moira swallowed. It was easier talking to a hallucination, however vivid. Assuming this was another hallucination. She wasn't sure and that frightened her. "Both. Mainly, mainly them."

"Because they betrayed you." She nodded. "Ah." He uncrossed his ankles, re-crossed them. "And me?"

Moira stared a moment. "You…it really has nothing to do with you."

"Yet you'd leave me anyway."

"Yes. It's for, for the best." She felt tears and there were two John Sheppards swimming in her vision, until she blinked and the two became one.

"And yet it's killing you."

"It will kill me if I don't leave…but I can't….I can't leave…" She looked away from him, up at the ceiling where the dim lights flickered, flickered. "I was so happy…too happy…and then the crash came and it has nothing to do with you and everything to do with me. They betrayed me, John! They all did! People always betray me and you'd think I'd learn by now but I guess I haven't yet. Oh I know I'm overreacting but I can't help the way I feel! And it has nothing to do with you, not really. You are a separate issue, distinct, apart from all of that but not quite, not quite. John, John, I don't know what to do and if it gets worse…if they all force me…if they all make me endure this again I don't think I can. John, what should I do? John?"

The chair was empty. She stared, lifting her head to look round in case he had moved and she had missed it, if he had even been there at all.

"John? John, please help me! John?"

A wave of dizziness assailed her and she fell into the depths of darkness once more.

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Jason stood.

He was waiting at the back of the Jumper, hands on the manual release above Ronon's as the Satedan gripped the cold metal. Jason's heart was beating fast. He tried to fight the anxiety as he waited for Colonel Sheppard to rescue them. Once the second Jumper's shield was extended to this ship the door could safely be opened and both men would race to freedom.

Hopefully before the fugly fired on this vessel.

This Jumper was devoid of all power, a sitting duck and vulnerable. Colonel Sheppard had a plan and although Jason did not know the plan it was good enough for him that the colonel had one. He tightened his grasp on the cold metal as sweat lined his palms.

"Reynolds, copy? Get that door open now!"

"Yes sir! Ronon, now!"

The two men grunted as they turned the release bar. It creaked in protest. Without any automated systems working it was hard work, but both men were sufficiently motivated. After a few swear words and turns the release snapped into place and the door opened.

A pinkish tunnel awaited them, surrounded on all sides by roiling ocean waters. At the end of the tunnel a Jumper waited, its hatch open and beckoning. The men did not hesitate. With a glance at each other they stepped into the shield, then ran to their rescue.

"Sir! We're almost there!"

"Move it, major, now! That fugly is almost here!"

"We're here!" Ronon shouted, shoving the other man ahead of him. He whirled to slam the hatch shut as the extended field quickly evaporated.

"Get up here now and hang on!" John called over his shoulder.

Jason and Ronon moved to the front of the ship as it hummed with power. John was seated at the controls. The HUD was a translucent screen in the air, revealing the proximity of the alien ship as it drew closer and closer to the damaged Jumper. John was watching it, scowling, hands on the controls as he waited, waited.

"Sir?"

"Good to see you, Sheppard."

John glanced at the two men, nodded. "Likewise. We'll be home in a sec. First we need to eliminate this threat."

"Sir? If you fire on them won't that alert them to our presence?"

"Not if it looks like an accident, or sabotage from the downed ship. The initial blast will shield us from any scans and we can hightail it back to Atlantis. Almost…almost…here we go. Firing Drones. I hate to lose a ship like this but we don't have much choice."

A phalanx of yellow squid-like Drones flew out of the Jumper and straight for the other Jumper. Just as the fugly submersible reached the vessel the missiles struck.

The explosion was silent, but enormous. It threw the imploding ship into the fugly submersible, effectively annihilating it. A wave plumed and threw back the Jumper, sending it backwards.

John knew this would happen and piloted the vessel backwards, riding the flow of expended energy before swerving to change course, turn round and speed back towards Atlantis. "Readings?" he barked, concentrating on keeping this ship stable and in one piece as churning water and uprooted coral were proving to be dangerous obstacles.

Jason checked the screens. "Both targets destroyed. Debris is everywhere, sir. I'm not detecting any scans…but our own readings are haywire."

"Are they dead?" Ronon asked.

"Yes."

The city came into view. It was a spectacular sight. It was like a castle with many towers enshrined under a pinkish dome. It was beautiful. It was inspiring.

It should have been full of light but it was dark. Too dark.

"Sir?" Jason saw the colonel's frown.

"That's odd. Rodney, do you copy? Rodney, we're heading for the underwater bay. Get ready to give over controls to me for shield penetration. McKay? Copy?" John tapped his earpiece. "Shit. We should be in radio range."

"Could be interference from the explosion, sir," Jason suggested.

"This far? Why is the city so dark?" Ronon was peering at the city, frowning. Something didn't feel right, and he knew that John felt it too.

"Maybe…I'll keep hailing him. If he doesn't do his part we're gonna hit this thing like a bug on a windshield," John warned.

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Rodney swore.

He was seated in the control room, trying to access the system but he kept being denied. It was as if the city was fighting him and he didn't like that, not one bit. Added to that the radios were full of static and distortions. "John, copy? Repeat that! Sheppard!"

He eyed the screens. He had seen the explosion. Alarms had weakly sounded but the shield was secure and intact. He could follow the Jumper that John was piloting as it made its way back, until the screen went black. He typed commands, accessing other systems but he kept receiving warning after warning after warning:

**ACCESS DENIED**

**SYSTEM UNABLE TO REBOOT**

**CODE NOT RECOGNIZED**

**DELETION OVERRIDE NOT RECOGNIZED**

"Damn it!" Rodney shoved back from the console, glaring at it. He had never had such trouble from the city, not like this. It was acting like a recalcitrant child, or as if the AI was sleeping, or missing, or only half there. He frowned at the thought. "Think you can get round me? I think not! You won't be getting round Rodney McKay that easily!"

He stood and considered. Grabbing his laptop he hastened to the conference room. The lights flickered then went dark, one by one as if the shadows were chasing him. Rodney was undeterred. His friend was out there, his friends needed his help and he wouldn't let them die out there! He rushed to the conference room as the doors were shutting, as if trying to keep him from his objective.

"Ha!" He barely got into the room. It was dark, only lit by the ambient glow of the computers. He produced a penlight and made his way to the keyboards sitting in front of the monitors. "Okay, okay, you can do this," he said to himself, wiping his sweaty palms on his thighs as he sat, staring. "I'll use the backdoor systems we initiated after the Replicators tried to take over the city. Radek and I installed a failsafe should something like that happen again."

He knew it was ridiculous to talk to himself out loud, that if anyone heard him they might think he was going crazy like Moira was, but he didn't care. He wondered if perhaps Moira wasn't so crazy after all, considering what was happening now. He entered the system, forcing himself past blockade after blockade, sneaking into secondary systems to worm his way to the primary ones.

A cold breath tickled the back of his neck. Engrossed in the equations he brushed it away, irritated and not having time to wonder what that was.

Or who.

"Rodney, what the devil are you doing?"

Rodney almost yelped at the voice, at the touch of a hand on his shoulder. He looked over to see Carson standing near. The doctor appeared angry. His blue eyes were ice, flaring and appearing to glow in the light from the computers. "Carson! How did you get in here?" Rodney's gaze darted to the door. It was still shut. He looked at the doctor. "I'm trying to access the shield system so John can get back into the city!"

"I don't think that's a good idea, Rodney. We're losing power as it is."

"What? No, we can't be!" Rodney shifted to another screen and stared. Power levels were dropping into the red, although no significant drain was detected. "How can that be happening?"

"I pulled the ZPMs."

"You what?" Rodney exclaimed, staring. "Why? Good God!" He whirled and his fingers flew over the controls. "I can activate one from here but the other…what the hell were you doing, Carson! John and Ronon and Jason are out there, possibly under attack from the fuglies! John is out there! John!"

"I know. Isn't it about time he learned his place? That you are the master of the city?"

"Have you gone insane?" Rodney protested, but he never quit working, not even when a coldness was enveloping him from Carson's iron grip on his shoulder. "You won't defeat me! I won't be defeated by an insane AI or a demented doctor! Move!" Rodney shoved Carson aside, shoved the cold grip off his shoulder.

"John! John, do you read? I'm giving over control now! Sheppard! John, we're under att—"

The rest was gone as a blow struck the side of Rodney's head. The physicist fell across the keyboards, then the floor. Blood was spilling from his cut lip. He moaned, trying to move but the floor was spinning.

"I told you not to interfere."

Rodney started as the voice didn't sound like Carson, not at all. It sounded distinctly female. A wave of cold swept over him, freezing him. He struggled against it as his head spun.

He fell back, helpless.

He waited, fighting the disorientation and pain. The coldness lessened. He felt the absence of Carson and whatever else had been with him. Rodney hauled himself up to his knees. One shaking hand crossed the keyboard and punched a button.

Before he could see if he had succeeded or not Rodney fell onto the floor, unconscious.


	3. Chapter 3

Stargate Atlantis: S7 The Fossil Key

Part Three: Mesopredator Release3

John was worried.

He didn't show it, but his companions knew nonetheless as they were equally worried. As the Jumper approached Atlantis at a quick pace nothing was happening. The light on the console was still red; until it jumped to green John had no control over the city's shield or any of the city's systems.

He was effectively orphaned in the ocean depths.

Atlantis was looming closer. It was a pink dome, a sponge about to absorb them, but instead of absorbing them it would crush them on impact unless the two shields merged harmoniously. Instead of welcoming the city appeared threatening. It was a giant monster about to crush them unless John could gain control and safe passage.

John licked his lips. "McKay, copy? Rodney, we really need that system control now. Stop showboating and hand over the system controls!" Anger flared briefly, but John knew his friend wouldn't deliberately leave him in the lurch like this unless something was seriously wrong. Would he? A doubt flickered and was gone.

The city appeared to be even darker. Only a few lights glimmered in the central core. They were bright spots winking against the pink shield, against the darkness of the ocean. They were lonely orbs of light in a sea of darkness. A few more winked out as the central tower became a dark beacon pointing upwards like a finger of doom.

"Sir? We're on the vector for the underwater bay. Hangar doors are closed." Jason's voice was subdued as he realized the severity of the situation. He had been rescued, only to be killed like this? He shook his head at the irony.

"McKay will do it. He will," Ronon stated. He had no doubt that Rodney would pull through; the physicist had saved their necks countless times and always at the last moment. He flexed his arms, feeling the need to move, to hit, to strike out at something.

"He better or I am going to drown him in lemons," John muttered. He dipped the Jumper lower. They were skimming just above the ocean floor, heading inexorably for the underwater bay. "McKay, copy? Major Banks-Dex, do you read? What the hell is going on in there?"

"Amelia will get us in," Ronon assured, but he felt a pang of worry over his wife. He knew she was more than competent and could take care of herself just fine, but still he worried. He wanted to hear her voice, at least.

"Shit. I can't slow down…it's like we're being pulled in!" John's hands shifted on the controls and he concentrated, but the Jumper was unable to respond. It whined in protest and alarms flared, warning John to stop fighting the automated system that was yanking them to the city.

"Sir!"

John nodded as the light flickered green. Without hesitating he increased the speed, riding the momentum that was tugging them to the city. He concentrated, slipping into the merge of man and machine to navigate the vessel. He tensed, lips pursed together as the response was even more sluggish, more combative but he fought, he commanded and the two shields met with a flare of sparks but safely joined.

The ship was cocooned in a bubble, but something was wrong as sparks struck and the shields weren't exactly merging as smoothly as they had on the outgoing trip. John concentrated, navigating the vessel towards the underwater bay. The hangar doors were slow to open; too slow as the ship was being abruptly tugged towards them, faster than John had intended.

It would smash against them like as ship floundering on the rocks if the doors didn't open.

"Damn it, what the hell? McKay, give over all control now! McKay! McKay! Shit! Brace for impact!"

"Sir?"

"We're gonna ram our way in, major. Hold on!"

"Do you know what you're doing, Sheppard?" Even Ronon sounded dubious.

"Of course not! But if we don't get in there now we will either explode out here or drown? Have a preference?" He glanced at his friend.

Ronon smiled. "Go for it."

"Thanks." John grimaced as he gripped the controls and concentrated, closing his eyes to mere slits. The vessel was responding readily enough but the city itself was being coy, refusing him like a coquettish woman who would flirt but wouldn't put out when it came down to it. John scowled at the thought, but brought his considerable charm to bear, cajoling and wooing silently.

He could almost see her now, a woman in white who was turned away from him but looking over her shoulder at him. She was beautiful, elusive and teasing but John was determined, more than determined to have her. He grunted as the rush of power filled him, as the sudden control of the interface filled him.

As at last she acquiesced to his desire with a playful dropping of her clothes.

"Sir? Wait! The doors are opening!" Jason exclaimed.

"Knew you could do it!" Ronon slammed his hand on John's shoulder.

"Fuck! I mean, yeah, yeah, here we go." John flew the Jumper through the doors, almost scratching the drive pod in his haste. He accelerated, flying up now and out of the ocean. Water streamed off the ship and splattered onto the walls. He flew across the floor, dropping the shield and landed the ship near the others.

He opened his eyes, sitting back, momentarily drained and puzzled and pissed all at once.

"Colonel Sheppard?"

John rubbed his forehead. He moved to his feet after powering down the ship. "Let's go see what the hell is wrong this time." He led the men out of the Jumper and paused. The lights were flickering wildly. He strode to a wall and touched it, pressing his palm along it and the lights became steady amber orbs.

"Ronon! Thank God! Ronon!" Amelia ran towards her husband, heedless of any military protocol. She slammed into him with a hug and Ronon grinned, happily returning it.

"Major, report," John said mildly, exchanging a glance with Jason.

"Sir? Sir." She freed herself from her husband, embarrassed. "I've been stuck in the lower levels trying to optimize our power. The city was in some kind of lockdown and I couldn't get out until now. I've lost radio contact with McKay."

John tapped his earpiece. "McKay? Rodney, please respond. Rodney?" He frowned. He looked round. The shadows seemed darker. The city felt colder. He looked at the others as a dread filled him, a dark suspicion. "Major Reynolds, get to the control room and secure it. Major Banks-Dex, get that ZPM working on full power. Ronon, go with her."

Before any could question or protest John was gone, sprinting out of the bay.

His hand was on his gun.

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John sprinted up the stairs, down the hallways, running in a city of darkness. He reached the control room and paused, but it was empty. He felt a chill that had nothing to do with being underwater. He moved to the consoles and activated them. Power hummed but it was weak. Lights flickered continuously.

John looked at the monitors. They were winking on and off, the displays hazy. As far as he could tell the fugly ship was returning to space, joining the other one in orbit. He whirled as Jason entered the room. The younger man appeared spooked.

"Sir?"

"Keep her running and keep trying to bring her online. I will find McKay."

John headed for the conference room. He froze in the doorway.

Rodney was sprawled on the floor, face first. The computers were blinking, blinking like eyes and shedding sporadic light onto his form.

"Rodney!" John rushed to him and moved to his knees in front of the physicist. Hearing a groan from the physicist relief swept through John. He turned Rodney onto his back. "Rodney! What the hell is going on? Are you okay? Rodney, here, take it easy!" He helped the moaning man into a chair.

Rodney touched his lip where dried blood was a scab tugging his skin. "Ouch! John? You made it? You made it! Thank God!" He grabbed the other man's arm, trying to focus on him. "He tried to stop me but at the last minute I switched the controls to you and you made it!"

"He? Who?" John asked, but he already knew.

"Carson. He's gone crazy! No! And then it wasn't Carson! It was some, some woman! John, it was some woman who was taking over the city and wanted you to die!"

"It was the city, Rodney…not a woman."

"What?" Rodney blinked several times. His friend kept swimming in and out of focus and his head was pounding like a drum. "It was a woman…but Carson was…I mean…the city? The AI! You mean the AI! How is that even possible unless there's a system wide failure and the back-up system is going haywire and John! You made it!"

"Yes, Rodney. Take it easy, okay?" John moved to the keyboard, typing commands. Power flared briefly then faded, unable to sustain the connection. "I think I know what's happening and it ain't good. In fact it's my fault."

"Yours? How? What is happening?"

"If I told you you would think I was crazy."

"Try me. And hey, you can't be crazier than Moira, right? Oh…sorry…" Rodney blanched as John glared at him, but his gaze slid over to the pad of paper a monitor. It was full of his writing, as he had been trying to decipher the messed up Morse code. He stared at it, recalling Moira's words about the code being backwards so the letters would be. He saw she had written lines backwards that were unreadable.

Except that they were readable on the dark computer screen as the overhead light reflected the writing onto it.

_WILL TAKE CITY ABSORB ONE MIND KILLMOIRA INTERFACE JOHN ATLANTIS RISE_

"John? John?"

Rodney's question was ignored as John whirled and ran out of the control room.


	4. Chapter 4

Stargate Atlantis: S7 The Fossil Key

Part Three: Mesopredator Release4

John was running.

The only sounds were John's footfalls as he ran through the hallways. His boots rang heavily on the floor as he ran. His heart was pounding in his chest and he could hear it as he rushed, dreading what he would find and trying to work his mind around what was happening to the city.

Mostly he feared he was too late.

Like he had been too late the last time.

He ran into the infirmary and stopped short. His breath caught in his throat as her name died on his lips. He stared.

The infirmary was an ocean of darkness. One light was flickering, flickering like a bad television screen, and like a horror movie it was shedding sporadic light on one bed where a figure lay. Where a woman was reclining, head rolled to one side. She was strapped to the bed by wrist and ankle restraints. Dried blood was a dark stain on the white sheets near her head.

"Moira."

The word finally escaped his lips, like a cold breath that sent a shiver up his spine. He quickly moved to her. He reached out a hand. It shook slightly as he touched her pale, pale cheek. His chest felt constricted and he couldn't breathe, couldn't think and he froze.

Until she softly, softly moaned.

Relief flooded John, a relief so palpable he felt tears. "Moira? Moira! Hang on, sweetheart, I'm here now!" Quickly he undid the restraints, one by one, hands gentle as he revealed the vivid bruising on her flesh. He moved round the bed as she stirred, moaning and moving slowly. "Hang on, baby, I'll get you outta here! What did they do to you, Moira? What did he do?" He glanced at the tray full of instruments and electrodes. He looked at her, seeing the marks on each side of her temple. Anger filled him, a fury that chased away the cold.

Moira opened her eyes and began to struggle. There was a man. His hands were on her, holding her down. The light was behind him and all she could see was his dark form. His features were obscured. "No, no, no, please, please, not again not again not again please!"

"Whoa, Moira, Moira it's me!" John caught her and helped her to a seated position.

"John?" She stared, grabbing his arm as the light revealed the alarm on his handsome face. "John? Are you, are you real?" she asked shakily.

"Yes, Moy, I am real. Moira." He lunged towards her and kissed her. It was a hot, fervent kiss. It was sloppy, passionate and warm. Their lips entwined, seeking and sucking. His lips parted hers and his tongue dove into her mouth, playing wickedly until the kiss ended.

Moira blinked as he pulled back from her. "Wow…okay. John!" She hugged him, fighting tears and the lethargy that was drowning her.

"Let's get you outta here, sweetheart. What the hell happened? Here, can you walk?" He helped her to her feet. "Where the hell is he?" he growled.

Moira swayed, holding onto his arm. She looked round fearfully. There was only darkness. "John? John, are you real?"

"Yes, Moy. Let's go." He guided her carefully out of the infirmary, alert for any danger. "Moy, let me carry you," he said as she stumbled.

"No! I can walk I can walk!" she insisted, voice quavering as pain shot up her legs. Her head was pounding but at least she was free, out of the restraints and away from that bed. And John was real, very real and solid and was helping her. "John!" she yelped in protest as he paused and swept her up into his arms.

"It's quicker this way and you are injured, Moy!" he said, losing patience. He wanted her someplace safe and fast. "Where is he?"

Moira clung to him, hiding her face against his shoulder as the darkness enfolded them. Lights weakly flickered as they moved down the hallways. She peeked over his shoulder. It looked as if the shadows were chasing them, but it had to be trick of the light. There were no Homo erectus, at least, and no other hallucinations.

"Moira? Where is he? What did he do to you?" John asked as they reached her room. He carried her to the bed and gently set her upon it. "Moy?" She was cold, so cold to the touch and pale, too pale as she stared up at him. He sat close to her, catching her hands in his. "Moira?"

For a few fateful heartbeats he feared he was too late.

"John! John, are you real?" she asked again, as if awakening from a trance. "No! I mean get me out of here! It wasn't Carson! I mean I mean it was but it wasn't! There something in him, John! There's something in him, orchestrating all of this! John!" She turned to face him, her nails digging into his arm to gain his attention after she looked round the room. "It's not Carson! It's something inside of him! I saw it! I saw her! I sa woman a a a—"

"The city. You saw the city, part of the AI," he confirmed quietly. He caught her as she swayed. Her brown eyes were huge and the purple ring around her pupil was vivid as if it was glowing as the light hit her face. "Don't you worry, sweetheart. I will get it out of him, one way or another." He eased her onto her back. "You rest now. You're safe now, Moira. Don't open the door to anyone but me, all right?"

"Where are you going?" she asked, clutching at his hands as he tried to free them from her.

"I'm going to take care of this, all right?" He leaned close and kissed her. "Don't be afraid, Moy. I'm here now. I'm sorry, I'm so sorry. I never should have left you. I never should have…" Emotion choked off his words and he looked away for a moment, mastering them.

"John? John, please don't go. John, please, please don't…" Her voice fell softly as the lethargy was making her limbs heavy. Pain was a constant in her wrists and ankles and head. Tears made her vision swim and made the one John into two Johns.

"Easy, Moy. I'll be back, I promise. You are safe here." He kissed her again and drew up a blanket over her. "Rest. Nothing else will happen to you, I swear."

"John…are you real? Are you…" Her eyes fluttered as she was having trouble keeping awake, as if the brief exertion getting to her room had been too much for her.

"I am real, Moira, and I love you."

John stood a moment, watching as Moira softly smiled. Her eyes closed. He turned to leave. He turned back again, debating. There was one thing he had to do before he left her.

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John strode purposefully through the hallways. He paused now and then, pressing his palm to the wall and activating the lights. He circled round and entered the infirmary. Without a word he strode up to Carson as the doctor was staring at the empty bed where Moira had been imprisoned.

Carson turned, hearing the distinct sound of boots on the floor. "John? John, you made it! Where the devil is—"

John's fist ended the sentence. He swung a vicious right hook into the doctor's face. Carson spun and landed hard onto the floor. Blood spewed out of his mouth.

"John, no! John!" Rodney ran to his friend, grabbing his arm before John could take another swing or do far worse.

"He hurt Moy! You should see what he did to Moy!" John growled, but now that he had vented his fury he forced himself to think before acting.

"What? What did he to do her? Carson?" Rodney asked in disbelief, but his sore jaw reminded him that Carson wasn't exactly the kindly doctor anymore. It was shocking and Rodney couldn't quite wrap his head around it. "Where is she now?"

"She's safe in her room. Help me get him up."

"Carson hurt…what? How?" Rodney's gaze darted to the tray of medical instruments and he felt a shudder, seeing the electrodes, seeing the restraints on the bed. "What are you going to do with him?" he asked, helping John pull the nearly unconscious doctor to his feet.

"We're gonna get the bitch outta him! Let's go!"

"Go? What bitch? Go where?" Rodney was completely baffled.

"The Chair," John replied tersely.

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"Anything?" Ronon asked. He was standing guard near his wife, keeping his gaze on the shadows and the darkness that surrounded them. The city was quiet; too quiet as not even the water was bubbling in the walls. It was creepy, and Ronon half-expected a Wraith to jump out of the shadows.

He would have preferred a Wraith to a fugly any day.

Amelia shook her head as she squatted near the ZPM container unit. "Nothing. It's got power, it's not damaged, but it's like something is blocking it! I need McKay down here! This isn't exactly my area of expertise!" she fumed. She pushed the ZPM back inside and checked the controls again. They were all dark but the readings were normal.

"Radios are still not working," Ronon reminded. "What happened here?"

"I'm not sure." Amelia sighed and moved to her feet. "It's weird. It's like the city is, is acting against itself. It's almost like it caught a computer virus and refuse to reboot. That doesn't make any sense, I know."

"Nothing much surprises me anymore. Let's go."

"Go? Colonel Sheppard said to stay here."

"You can't fix it. Let's see if Reynolds can do anything in the control room. We need to round up all of our people."

"Ronon? What happened out there?" she asked, catching his arm.

"Not much," he admitted. "We had to blow up a fugly ship that was underwater."

"You what?"

"We didn't have a choice, and it will look like a self-destruct on ours. That landing party was beamed up, so I am guessing they didn't find what they were looking for."

"You think they might move on?" she asked, following him out of the room. "Ronon, tell me exactly what happened out there!"

"I'll tell you on the way. Let's move."


	5. Chapter 5

Stargate Atlantis: S7 The Fossil Key

Part Three: Mesopredator Release5

John worked quickly.

He eased Carson into the Chair and grabbed a set of wires to tie the doctor in place. Carson was moaning as he regained consciousness. John ignored him, quelling the urge to beat the doctor senseless, trying to keep reminding himself that it hadn't been Carson torturing Moira. It had been whatever was inside him.

Rodney knelt near the two Chairs, quickly activating the interface between them and hooking them up to work in tandem. His fingers fumbled and his vision blurred but he worked past all of that, trusting that John knew what to do. "And this will, um, free him?"

"It will get the entity out of him, yes, and once he's Carson again get him out of that Chair and you two run to the control room and lock it down."

"What? Why? John!" Rodney stumbled to his feet as John was now placing blocks of C4 onto the second Chair where Carson was sitting. "What the hell are you doing?"

"I created this. I need to end this now." John circled the Chair. "The city can't handle two AIs and it is going crazy. I should have realized before this!"

"The city? You mean...you mean that other city's AI was in the Chair and now—"

"It's in Atlantis but Atlantis can't handle two AIs. It's like having two conscious minds in one brain."

"Oh. Been there done that. OH! That almost killed me!"

"Exactly, and it almost drove you crazy before that. The same thing is happening here, but it's worse because they are both competing for..for control." John had almost said they were competing for him. In a way they were, and it wasn't unusual to have women competing for him. Normally it didn't involve the fate of a city, however.

"What do you need me to do?"

John got into the Ancient Chair. Power flared and it reclined, enfolding him with the interface. "Get as much power here as you can, all the power from the secondary systems. Once Carson is clear get him to the control room and lock it down."

"What about you? If that Chair blows—"

"Never mind about me! I can protect myself." Before Rodney could protest a blue force field rose from the floor and surrounded John and the Chair.

"Wow…I didn't know it could do that! How did you—"

"If I can't get the city under control and destroy that other AI you will have to take control and purge all of the systems!"

"NO! If I do that and you are in there—"

"I know." He met his friend's gaze. The severity of the situation hung between them. "Just do it, Rodney, or we're all gonna die down here."

"I…okay. Once you are out and only if you can't—"

"No! Don't you dare fucking wait for me! Purge all the systems once the Chair is destroyed and you have the primary functions online. That is a direct order!"

"John? Rodney? What the…where am I?" Carson looked round, dazed. He struggled, finding himself tied to the second Chair. He couldn't remember how he had gotten there, or why he was in the Chair. "What's going on?"

"You'll be better soon, doc. Just relax." John flexed his fingers and rested his hands on the pads, readying himself.

"Relax? What the hell are you doing, John? Rodney, get me out of here now! Clearly John is delusional and having some sort of psychotic episode! Rodney!"

Rodney shook his head, moving round to squat behind the Chairs where the power was flaring. He flicked switches. He attached the ZPM to both. "If he is then I am as well. Hang on, Carson."

"Hang on? What the bloody hell are you doing to me?"

"Payback's a bitch, doc," John said with a smile. He closed his eyes and delved into the interface.

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Jason paced repeatedly. He had done what he could and now stood guard, watching the systems as the power flickered and surged and waned. The screens were full of information until they went blank. Jason couldn't keep still. He held onto his P90 although he didn't know what the threat was. All the same he kept it close and circled the control room.

An unseen enemy was far worse than any he could imagine.

He whirled, raising his gun hearing footsteps and voices. He lowered the gun as Ronon and Amelia entered the control room. "What's happening?"

"I was going to ask you that!" Amelia stepped to a console and began to ply the keyboard. "At the very least I can get the comms up, citywide. Colonel Sheppard, copy? Doctor McKay, do you read?" she almost shouted into the PA unit. Her voice blared loudly in the air, intercut by static and a weird hissing sound that almost sounded like laughter.

Ronon glanced round the room then moved to a screen. "Can you locate them on this?" He rued his ability to use the computers and realized he should learn at long last.

"Maybe. Let me try. The readings are so sporadic." Jason moved to the screen and worked, typing and attempting to access information that should have been right at his fingertips.

Amelia shook her head. "As far as I can tell those two fugly ships are still in orbit, but they haven't made a move towards us. Ronon, are you sure that fugly submersible was obliterated?"

"Yes, as was the other Jumper. They must have detected that."

"Then why are they still sitting there?" she mused. She tapped the audio again. "Colonel Sheppard, please respond! Doctor McKay, do you read?"

"I've got three life signs in the Chair room but there's some kind of energy ow!" Sparks flew and Jason fell backwards as the monitor overloaded.

"Shit! Ronon!" Amelia shouted.

Ronon was already moving to grab a fire extinguisher. He rushed to spray the foam over the explosive components before the whole console ignited. "Got it! Reynolds?" Ronon turned to see the major sprawled on the floor.

A vicious cut was bleeding on his forehead.

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"No! Get me out of this Chair, damn you! Let me go!" Carson shouted, struggling. The bonds held him fast as the Chair reclined. He had no control over it and he fumed, glaring at John. "You son of a bitch! What the hell do you think you are doing?"

"_What the hell do you think you are doing?" the woman demanded. She was furious, glaring at John as she stood in front of him. She was beautiful, fiery, her hair a red fall of tangles amid the flowing white of her gown. She lifted a slender arm and pointed at him._

"Get me out of this Chair now! I won't let you destroy this city! I am in control! I won't let you destroy me!"

"_I won't let you destroy me!" the woman shrieked. She advanced, a beautiful vision in white with blond, curling hair and ice blue eyes. Blue eyes so cold they were chilling. Her words dripped with vehemence and her voice jangled like icicles along John's skin. _

"I was trying to help her, you fool! Getting revenge on me won't bring her back! You will never be able to bring her back! I won't let you go!"

"_I won't let you go! We won't let you go!" the two women threatened in chorus. Like Greek furies they advanced, hair flying, arms extended and hatred on their beautiful faces. Cold laced them, swirled around them and whispered along John as he stood, facing them._

Rodney jumped to his feet, ran around as heard Carson's voice, than a woman's voice. He stared as for a brief second he saw a woman's form merging with Carson's, screaming until it was violently pulled out of him and into the Chair. Power flared brightly, so brightly that the physicist had to shield his eyes.

"John? Rodney? What's going on? Where am I?"

"Carson!" Rodney moved to his friend. The doctor was pale, disorientated but his blue eyes were his own. "Is that really you?"

"What? Of course it's really me! What's going on? What the…" Carson stared at the force field encompassing the Ancient Chair where John reclined. "John? What's he doing?"

"Saving you. Saving us! Come on! We don't have much time!" Rodney quickly unstrapped the doctor and hauled him out of the second Chair. The lights on the C4 blocks were blinking, indicating the countdown had begun.

"What's he doing? What…oh my God…I remember…Moira…what I did to…" Carson's anguish flooded him and he almost crumpled, but Rodney hit his arm.

"Buck up, Carson! We don't have time for that! Get to the control room and lock it down! I'll be there in a second! We'll have to do a purge if John can't get the AIs to merge!"

"The what? What about John? You can't leave him there!"

"I know! Go! I'll make sure he can get out!"

"How?"

"Just go! I'll be right behind you!"

As Carson ran out of the room Rodney whirled and moved to the interface. The power was surging, surging and the ZPM was glowing like flames. "Damn it, John, you better be right about this! I won't let you sacrifice yourself, I just won't!" He disconnected the second Chair and moved round to face his friend.

John was moving in the Chair, his handsome face contorted with both pain and determination. He was unreachable, as the force field effectively blocked all intervention, and he was so deep into the interface now any attempt to disconnect him would prove fatal. Rodney pondered what to do, his mind racing over previous attempts and he realized what he had to do.

He ran out of the Chair room.

The minutes counted down to seconds.

The seconds counted down rapidly.

Boom.


	6. Chapter 6

Stargate Atlantis: S7 The Fossil Key

Part Three: Mesopredator Release6

The second Chair exploded.

It was exactly on time. The C4 ignited and with a tremendous blast the second Ancient Chair, the one that had been taken from a sister city of Atlantis was torn apart. The blast radius encompassed the entire room. Pieces of the Chair flew in every direction, smashing into walls and slamming up into the ceiling. The Chair was uprooted from the floor where it had been bolted and the blast ripped up the floorboards, gutting that section almost to the next level beneath it.

The pieces bounced harmlessly off the force field surrounding the first Ancient Chair. If John had opened his eyes he would have seen a spectacular display of sparks and lights, like a mini-nebula had come to life in the room. Colors spiraled and danced as energy met energy and fought a vicious battle for dominance.

Much like the battle John was facing as he was ensconced in the interface.

He couldn't open his eyes. He was locked in the Chair, gripped by the power and driven by sheer stubbornness to see this through, to take back control of the city and to heal the AI no matter what the cost was to himself.

He was locked in a virtual reality, facing down two very angry and psychotic AIs who appeared as women to him. Two women who were battling for dominance and who were battling for him. His ATA was the link they needed, the ultimate interface of man and machine. They were like two sisters or two halves of a single entity that couldn't exist together, not in the same city. The systems couldn't take it and John had a choice to make.

He had to figure out how to join them together, or kill one of them.

Even if the cost was his own life.

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Moira woke.

She sat up abruptly, not knowing how long she had been asleep. A loud noise had interrupted her exhaustion and she stared round, not knowing where she was. As the panic subsided she recognized the confines of her room. She was safe. John had saved her. John had freed her from the restraints and taken her out of the infirmary. She eyed her bruised wrists as her head was sore. A dull ache consistently pounded, pounded.

She stared at her left hand. There was a ring on her fourth finger. She didn't recognize it. She stared, bringing it close to her face as her vision swam in and out of focus. The ring was gold. There was a round diamond on it. The emergency lights flickered over the gem and it sparkled at her. She stared, having no idea how it had gotten there. It wasn't hers. Was it?

She lowered her hand and moved shakily to her feet. Power was humming in the floor, in the walls. The floor seemed to cant and she caught herself, made her way to the bathroom. She turned on the light and washed her face. She drank greedily. The water was cold, refreshing. She stared at herself in the mirror. She looked strange, haunted, pale; a shadow of her former self. She wondered if she was real at all; if any of this was real.

She feared she was still strapped to that bed and that this, this was a dream, a hallucination.

She eyed the ring again. It wasn't hers, unless this was some alternate reality where it was hers. She looked up and gasped, whirled. There had been a man in the mirror; a dour reflection of a man standing behind her, all in black and glowering at her. A tall man with a lean form.

But there was no one behind her.

She grabbed the glass to drink again when an abrupt knocking on the door startled her. She dropped the glass to the floor. It shattered, pieces of glass flying everywhere. She knelt to the pieces to gather them, to hide from the pounding on the door, suddenly fearful lest it was Carson or someone else coming to return her to that bed.

"Moira! Moira, open the door! Moira, open the door!" Rodney shouted, hitting it with his fist. He frowned, looking up and down the hallway as the lights danced and the walls shook. "Moira!" He waved his hand over the panel but it wasn't working on this side.

Moira cowered, hands moving. "Ouch!" She looked down to see a large piece of glass had cut her wrist. She stared at the blood oozing from the opening in her skin, at the protruding glass sticking out like an exclamation point. She pulled it out and stared, stared as darker thoughts surfaced. It was an easy way to end it all; to end the confusion and the despair and the hallucinations. To spare John from what was only getting worse and there was nothing to be done about it. Nothing.

Nothing.

"Moira! For God's sake open the damn door! I need you! John needs your help!" Rodney argued, wondering if he could override the door mechanism even with the power fluctuations. "Open the damn door! John needs you!"

Hearing John's name she moved to her feet. She pulled out the shard and wrapped her wrist with a washcloth. She moved to the door and hesitated, recalling John's warning but she opened the door anyway. She blinked, staring. "Rodney?"

"Moira! About time! What did you do?" he asked, seeing the washcloth around her wrist. The material was turning crimson. He met her gaze as suspicion turned to realization to shock.

"Nothing. What—"

"No time! Come on!" Rodney grabbed her arm and pulled her out of the room. "You're the only one who can pull John out of the interface before it's too late! If he doesn't get out now he may die in there as he repairs the city and merges the AIs!"

"What? I don't understand!" she complained, pulled into a run next to the physicist. The floor surged under them and bucked as if the city was rising off the ocean floor.

"There isn't time! You need to get him out of there once I can disconnect the force field! If we can't get him out of there, Moira, we will lose him forever!"

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_John held an Ancient weapon as he moved backwards to the consoles. "I am in control of this city! Got it! You will obey me! Either join me or die!"_

_The women hissed at him, approaching. The city was whirling around him; things were flying in the air. John ducked and activated systems, using his codes to restore systems and activate the self-destruct. "You won't kill us. You won't destroy the city!"_

"_I will if it means destroying you!" He tapped the button and saw the time begin to count down. "There! This city will implode! Is that how you want it? If you help me we can raise Atlantis and take out those fuglies once and for all!"_

"_You will join with me, John Sheppard," the blond woman cooed, nearing with a smile. Her blond hair was golden in the light. "You are my chosen one. Join me and we can do whatever you want. You will rule this city with me."_

"_I already rule this city, bitch, and you will obey me!"_

"_You are wise to deny her, John Sheppard. She would kill the one you love," the red-haired woman agreed, nearing him on the other side. "I will help you rule this city and we can destroy the aliens once and for all."_

"_Ah, no, you're the reason this whole system's gone haywire. You should have died with Tir na nOg." As they lunged John shot one, then the other, then was blown backwards as they screamed in unison. He staggered watching as they shook and shimmered, merging closer and closer, becoming one blurry image that was shrieking wildly._

_John's head was pounding but he couldn't look away as the two shook violently side to side, becoming closer and closer and then becoming one frenetic image of a woman with two heads; of a brain with two minds, each screaming in unison and conflict._

_The scream went on and on and on and the images were whirling so fast that they were painful, as painful as that endless scream._

_It was a scream of the damned; it was a scream of insanity, of utter madness._

_John tried to cover his ears as it felt like his own head was splitting in two. He glanced at the monitor on the console and read the words of the program he had initiated._

_**SELF DESTRUCT IN THREE…TWO…ONE…**_

_John closed his eyes as Atlantis exploded._


End file.
